Dear All,

In order to figure out the Mean Inner Distance between Mate Pairs of my paired-end RNA-seq datasets, I ran Bowtie (Map with Bowtie for Illumina) with both forward and reverse datasets and mouse mm9 as reference genome. Below I list the Bowtie output for only one pair of reads (I put the fields on the left side):

 

For the forward read

QNAME:   SRR322837.8.1

FLAG:    99

RNAME:   chr1

POS:     163761156

MAPQ:    255

CIAGR:   36M

MRNM:    =

MPOS:    163761301

ISIZE:   181

SEQ:     NTGGATACTATTTTGCCATAAAAAAATGAATAAAAT

QUAL:    %(,,')(())@@@2235885<<22222@@@######

OPT:     XA:i:1 MD:Z:0A35      NM:i:1

 

For the reverse read

QNAME:   SRR322837.8.2

FLAG:    147

RNAME:   chr1

POS:     163761301

MAPQ:    255

CIAGR:   36M

MRNM:    =

MPOS:    163761156

ISIZE:   -181

SEQ:     TATTATGTCAATCTATGAAGAAGGACGGCGAGGTGA

QUAL:    GDBE@B>EEGDB=BD-=GG>GGGEDDG<GBGD8GB?

OPT:     MD:Z:29A6      NM:i:1

 

Is the ISIZE the insert size? The difference between POS and MPOS is 145bp, which is 36bp shorter than ISIZE (181). My question is: if ISIZE does mean insert size, how should I convert INSIZE into Mean Inner Distance between Mate Pairs?

 

Thanks,

 

Jianguang Du